Parenting and deformation
This sounds like you may have you have already 'Posed' your armature. 

When an armature is already posed, parenting somthing to it will cause the child to take on the armatures pose. You need to only use 'edit mode' for choosing how the armature is set up. However this can be fixed:

Select the armature, go to pose mode, then Ax2 (or 1) just to select all bones. Then hit Alt+R, Alt+G, Alt+S, to clear all data on the bones. 

When this is done your armature won't be where you wanted it, so go to edit mode to fix it back to the way you wanted.